Secondary sequence databases

Search WWW for a list of available secondary sequence databases of proteins. 

Secondary sequence databases (information extracted and summarized from primary databases) ... 

Databases are electronic filing cabinets that serve as a convenient and efficient means of storing vast amounts of information. An important distinction exists between primary (archival) and secondary (curated) databases. The primary databases represent experimental results with some interpretation. Their record is the sequence as it was experimentally derived. The DNA, RNA, or protein sequences are the items to be computed on and worked with as the valuable components of the primary databases. The secondary databases contain the fruits of analyses of the sequences in the primary sources such as patterns, motifs, functional sites, and so on. Most biochemical and/or molecular biology databases in the public domains are flat-file databases. Each entry of a database is given a unique identifier (i.e., an entry name and/or accession number) so that it can be retrieved uniformly by the combination of the database name and the identifier. 

There are different classes of protein sequence databases. Primary and secondary databases are used to address different aspects of sequence analysis. Composite databases amalgamate a variety of different primary sources to facilitate sequence searching efficiently. The primary structure (amino acid sequence) of a protein is stored in primary databases as linear alphabets that represent the constituent residues. The secondary structure of a protein corresponding to region of local regularity (e.g., a-helices, /1-strands, and turns), which in sequence alignments are often apparent as conserved motifs, is stored in secondary databases as patterns. The tertiary structure of a protein derived from the packing of its secondary structural elements which may form folds and domains is stored in structure databases as sets of atomic coordinates. Some of the most important protein sequence databases are PIR (Protein Information Resource), SWISS-PROT (at EBI and ExPASy), MIPS (Munich Information Center for Protein Sequences), JIPID (Japanese International Protein Sequence Database), and TrEMBL (at EBI). ... 

R. Lflthy, A. D. McLachlan, and D. Eisenbeig. Secondary structure breed profiles use protein sequence database for structural similarities. Proteins 70 229-239 (1991). 

Introduction to Molecular Biology Databases. 1994-2004. R. Apweiler, R. Lopez, B. Marx, UniProt, SWISS-PROT, Switzerland. URL http //www.ebi.ac.uk/swissprot/Publications/ mbdl.html. Contents include bibliographic, taxonomy, nucleotide sequence, genetic, and protein sequence databases PIR, SWISS-PROT, and TrEMBL, and specialized protein, protein sequence, secondary protein, and structme databases. 

Reliable secondary structures can enhance the prediction of higher order protein structure, and to a limited extent, secondary-structure motifs can even suggest specific fold structures. Sometimes these secondary structures provide insight into function. Definition of Secondary Structure of Proteins (DSSP), Integrated Sequence-Structure Database (ISSD), Protein Secondary Structure Database (PSSD), and CATH are covered in this section (see Table 2.2). 

GenBank has become a major sequence resource containing 150 million sequence records in 2009 and giving rise to hundreds of secondary, specialized databases worldwide. More than 500 milhon records in thirty-plus secondary databases exist at the National Center for Biotechnology Information alone. Worldwide, the number of bioinfor-matics records based on GenBank is in the billions. 

The archives contain atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors and NMR experimental data. Annotations in the structure entries include amino acid or nucleotide sequences (with notes of any conflicts between the structure in the PDB and sequence databases), source organism from which the biological material was derived, references to papers, secondary structure, complexes with small molecules included within the structure, etc. Third party annotations include images and movies of structures, pointers to other databases which contain information on the structural class or family of the particular structure pointers to particular specialized databases (maintained by others) such as the kinase , esther , or obsolete entries databases, and those that provide additional experimental information such as NMR and other solution data, abstracts of articles, etc. 

Homologous proteins have similar three-dimensional structures. They contain a core region, a scaffold of secondary structure elements, where the folds of the polypeptide chains are very similar. Loop regions that connect the building blocks of the scaffolds can vary considerably both in length and in structure. From a database of known immunoglobulin structures it has, nevertheless, been possible to predict successfully the conformation of hyper-variable loop regions of antibodies of known amino acid sequence. 

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